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Iron in PDB 4d38: Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

Enzymatic activity of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine

All present enzymatic activity of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine:
1.14.13.39;

Protein crystallography data

The structure of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d38 was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.170 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.870, 106.020, 156.340, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23

Other elements in 4d38:

The structure of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Arsenic (As) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine (pdb code 4d38). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine, PDB code: 4d38:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4d38

Go back to Iron Binding Sites List in 4d38
Iron binding site 1 out of 2 in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:27.3
occ:1.00
 FE A:HEM500 0.0 27.3 1.0
NB A:HEM500 1.9 19.1 1.0
NA A:HEM500 2.0 32.0 1.0
NC A:HEM500 2.0 27.7 1.0
ND A:HEM500 2.1 25.2 1.0
N01 A:L5Z800 2.2 37.9 1.0
SG A:CYS186 2.4 31.4 1.0
C4B A:HEM500 2.9 26.9 1.0
C1B A:HEM500 3.0 22.2 1.0
C1C A:HEM500 3.1 26.6 1.0
C4A A:HEM500 3.1 30.4 1.0
C1A A:HEM500 3.1 29.0 1.0
C02 A:L5Z800 3.1 39.5 1.0
C4D A:HEM500 3.1 23.6 1.0
C4C A:HEM500 3.1 30.3 1.0
C1D A:HEM500 3.1 27.7 1.0
CB A:CYS186 3.3 36.7 1.0
C05 A:L5Z800 3.4 38.5 1.0
CHC A:HEM500 3.4 25.0 1.0
CHB A:HEM500 3.4 28.7 1.0
CHA A:HEM500 3.4 28.0 1.0
CHD A:HEM500 3.5 28.8 1.0
CA A:CYS186 4.1 30.6 1.0
C3B A:HEM500 4.2 27.6 1.0
C2B A:HEM500 4.2 23.0 1.0
N03 A:L5Z800 4.2 41.2 1.0
C3A A:HEM500 4.3 26.4 1.0
C2A A:HEM500 4.3 30.6 1.0
C2C A:HEM500 4.3 26.3 1.0
C3C A:HEM500 4.3 28.7 1.0
C3D A:HEM500 4.3 26.8 1.0
C2D A:HEM500 4.4 25.8 1.0
NE1 A:TRP180 4.4 25.5 1.0
C04 A:L5Z800 4.5 38.9 1.0
C A:CYS186 4.9 34.4 1.0
N A:GLY188 4.9 28.2 1.0
N A:VAL187 5.0 31.8 1.0

Iron binding site 2 out of 2 in 4d38

Go back to Iron Binding Sites List in 4d38
Iron binding site 2 out of 2 in the Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Bovine Endothelial Nitric Oxide Synthase Heme Domain in Complex with (1R,2R)-2-(3-Fluorobenzyl)-N-{2-[2- (1H-Imidazol-1-Yl)Pyrimidin-4-Yl]Ethyl}Cyclopropanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.3
occ:1.00
 FE B:HEM500 0.0 32.3 1.0
ND B:HEM500 2.0 31.3 1.0
NB B:HEM500 2.1 33.1 1.0
NC B:HEM500 2.1 27.8 1.0
NA B:HEM500 2.1 38.6 1.0
N01 B:L5Z800 2.2 28.5 1.0
SG B:CYS186 2.3 32.2 1.0
C4D B:HEM500 3.0 37.3 1.0
C1D B:HEM500 3.0 34.4 1.0
C4C B:HEM500 3.1 30.3 1.0
C4B B:HEM500 3.1 35.9 1.0
C1C B:HEM500 3.1 32.5 1.0
C1A B:HEM500 3.1 37.0 1.0
C02 B:L5Z800 3.1 28.2 1.0
C1B B:HEM500 3.1 34.7 1.0
C4A B:HEM500 3.2 32.4 1.0
C05 B:L5Z800 3.2 34.1 1.0
CHD B:HEM500 3.4 34.2 1.0
CHA B:HEM500 3.4 34.1 1.0
CHC B:HEM500 3.4 35.6 1.0
CB B:CYS186 3.5 37.6 1.0
CHB B:HEM500 3.5 32.2 1.0
CA B:CYS186 4.2 36.9 1.0
N03 B:L5Z800 4.2 31.0 1.0
C3D B:HEM500 4.3 32.9 1.0
C2D B:HEM500 4.3 33.8 1.0
C3C B:HEM500 4.3 34.0 1.0
C2C B:HEM500 4.3 32.9 1.0
C3B B:HEM500 4.3 37.6 1.0
C2B B:HEM500 4.3 35.0 1.0
C2A B:HEM500 4.3 38.2 1.0
C04 B:L5Z800 4.3 32.1 1.0
C3A B:HEM500 4.4 34.5 1.0
NE1 B:TRP180 4.5 30.5 1.0
N B:GLY188 4.9 26.8 1.0
C B:CYS186 5.0 31.3 1.0

Reference:

P.Mukherjee, H.Li, I.F.Sevrioukova, G.Chreifi, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Novel 2,4-Disubstituted Pyrimidines As Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. 2014.
ISSN: ESSN 1520-4804
PubMed: 25489882
DOI: 10.1021/JM501719E
Page generated: Mon Aug 5 01:07:48 2024

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